Jimmy's always just assumed Kramer was on the roof and never gave it a second thought. Jerry yelling out the window was probably just much quicker than having Kramer come in, or Jerry making a phone call just for that one short line.
As for apartment numbers, they probably just never figured the show would become such a major television icon, and that details woud be scrutinized so closely. There are probably as many inconsistencies on Cheers, and every other show ever made as well, but they're not followed as closely, repeatedly analyzed, and discussed, as Seinfeld is. It makes us feel good to spot errors made by geniuses. But their priorities were better aimed toward other things, than say... props mysteriously moving, and multiple characters having the same apartment numbers. Hell, a Coca-Cola can has an appearance in the movie "Gladiator!"